Origin and Population Dynamics of a Novel HIV-1 Subtype G Clade Circulating in Cape Verde and Portugal

The human immunodeficiency virus type 1 (HIV-1) subtype G is the most prevalent and second most prevalent HIV-1 clade in Cape Verde and Portugal, respectively; but there is no information about the origin and spatiotemporal dispersal pattern of this HIV-1 clade circulating in those countries. To this end, we used Maximum Likelihood and Bayesian coalescent-based methods to analyze a collection of 578 HIV-1 subtype G pol sequences sampled throughout Portugal, Cape Verde and 11 other countries from West and Central Africa over a period of 22 years (1992 to 2013). Our analyses indicate that most subtype G sequences from Cape Verde (80%) and Portugal (95%) branched together in a distinct monophyletic cluster (here called GCV-PT). The GCV-PT clade probably emerged after a single migration of the virus out of Central Africa into Cape Verde between the late 1970s and the middle 1980s, followed by a rapid dissemination to Portugal a couple of years later. Reconstruction of the demographic history of the GCV-PT clade circulating in Cape Verde and Portugal indicates that this viral clade displayed an initial phase of exponential growth during the 1980s and 1990s, followed by a decline in growth rate since the early 2000s. Our data also indicate that during the exponential growth phase the GCV-PT clade recombined with a preexisting subtype B viral strain circulating in Portugal, originating the CRF14_BG clade that was later disseminated to Spain and Cape Verde. Historical and recent human population movements between Angola, Cape Verde and Portugal probably played a key role in the origin and dispersal of the GCV-PT and CRF14_BG clades.

人类免疫缺陷病毒1型（HIV-1）G亚型在佛得角为流行率最高的HIV-1进化支，在葡萄牙则为第二流行的HIV-1进化支；但目前尚无针对这两个国家内流行的该HIV-1进化支的起源与时空传播模式的相关研究。为此，本研究采用最大似然法（Maximum Likelihood）以及基于贝叶斯溯祖（Bayesian coalescent）的分析方法，对1992年至2013年这22年间，采集自葡萄牙、佛得角以及西非和中非另外11个国家的578条HIV-1 G亚型pol基因序列进行了分析。分析结果表明，来自佛得角（80%）与葡萄牙（95%）的绝大多数G亚型序列共同构成了一个独立的单系进化支（本文将其命名为GCV-PT）。GCV-PT进化支可能起源于1970年代末至1980年代中期病毒从中非单次迁移至佛得角，随后在数年内快速传播至葡萄牙。对在佛得角和葡萄牙境内流行的GCV-PT进化支的种群历史进行重建后发现，该病毒进化支在1980年代至1990年代经历了指数增长阶段，自2000年代初起增长速率逐渐下降。本研究数据还显示，在指数增长阶段，GCV-PT进化支与葡萄牙境内预先流行的B亚型病毒株发生重组，产生了CRF14_BG进化支，该支系后续传播至西班牙与佛得角。安哥拉、佛得角与葡萄牙之间的历史及近期人口流动，可能在GCV-PT和CRF14_BG进化支的起源与传播过程中起到了关键作用。